convertBAM2BigWig: Extract CTSSs from BAM-files (EXPERIMENTAL)

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

Function for converting mapped reads in BAM-files to CAGE Transcription Start Sites (CTSSs) in BigWig-files. Currently, this function will simply load a (single-end) BAM-file (respecting a supplied ScanBamParam), optionally remove short tags, and count the number of 5'-ends at each bp. Note, the BAM-file is loaded as a single object, so you must be able to keep at least one complete BAM-file in RAM.

Usage

convertBAM2BigWig(input, outputPlus, outputMinus, minLength = 1L, ...)

Arguments

input	character: Path to input BAM-file
outputPlus	character: Path to output BigWig-file holding CTSSs on the plus strand.
outputMinus	character: Path to output BigWig-file holding CTSSs on the minus strand.
minLength	integer: Minimum length of mapped reads.
...	Additional arguments passed to rtracklayer::import. This will often include a ScanBamParam

Value

Number of CTSSs/Tags returned invisibly.

Note

WARNING: This function is experimental, has not been thoroughly tested, and will most likely significantly change in upcoming CAGEfightR version. For comments/question please go to the CAGEfightR github page.

Examples

# TBA

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.